Merge branch 'main' into brendt/trace

.github/workflows/check_files.yml

@@ -11,7 +11,7 @@ jobs:
     - name: checkout
       uses: actions/checkout@v4
     - id: files
-      uses: Ana06/get-changed-files@v2.2.0
+      uses: Ana06/get-changed-files@v2.3.0
       continue-on-error: true
     - run: |
        for f in ${{ steps.files.outputs.added }}; do

.github/workflows/pytest_ubuntu.yml

@@ -113,7 +113,9 @@ jobs:
           coverage combine coverage?/.coverage
           coverage report
           coverage xml
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
           env_vars: OS,PYTHON
           fail_ci_if_error: false

scico/linop/xray/astra.py

@@ -141,7 +141,7 @@ def volume_coords_to_world_coords(idx: np.ndarray, vol_geom: VolumeGeometry) ->
 
 def _volume_index_to_astra_world_2d(idx: np.ndarray, vol_geom: VolumeGeometry) -> np.ndarray:
     """Convert a 2D volume coordinate into a 2D world coordinate."""
-    coord = idx[..., [2, 1]]  # x:col, y:row,
+    coord = idx[..., [1, 0]]  # x:col, y:row,
     nx = np.array(  # (x, y) order
         (
             vol_geom["GridColCount"],

scico/test/linop/test_convolve.py

@@ -76,6 +76,15 @@ def testobj(request):
     yield ConvolveTestObj()
 
 
+def test_init(testobj):
+    with pytest.raises(ValueError):
+        A = Convolve(input_shape=(16, 16), h=testobj.psf_A)
+    with pytest.raises(ValueError):
+        A = Convolve(input_shape=(16,), h=testobj.psf_A, mode="invalid")
+    A = Convolve(input_shape=(16,), input_dtype=None, h=testobj.psf_A)
+    assert A.input_dtype == testobj.psf_A.dtype
+
+
 @pytest.mark.parametrize("operator", [op.mul, op.truediv])
 def test_scalar_left(testobj, operator):
     A = operator(testobj.A, testobj.scalar)

scico/test/linop/xray/test_astra.py

@@ -8,7 +8,6 @@
 import scico.numpy as snp
 from scico.linop import DiagonalStack
 from scico.test.linop.test_linop import adjoint_test
-from scico.test.linop.xray.test_svmbir import make_im
 
 try:
     from scico.linop.xray.astra import (
@@ -30,6 +29,17 @@
 RTOL_GPU_RANDOM_INPUT = 1.0
 
 
+def make_im(Nx, Ny, is_3d=True):
+    x, y = snp.meshgrid(snp.linspace(-1, 1, Nx), snp.linspace(-1, 1, Ny), indexing="ij")
+
+    im = snp.where((x - 0.25) ** 2 / 3 + y**2 < 0.1, 1.0, 0.0)
+    if is_3d:
+        im = im[snp.newaxis, :, :]
+    im = im.astype(snp.float32)
+
+    return im
+
+
 def get_tol():
     if jax.devices()[0].device_kind == "cpu":
         rtol = RTOL_CPU
@@ -70,6 +80,31 @@ def testobj(request):
     yield XRayTransform2DTest(request.param)
 
 
+def test_init(testobj):
+    with pytest.raises(ValueError):
+        A = XRayTransform2D(
+            input_shape=(16, 16, 16),
+            det_count=16,
+            det_spacing=1.0,
+            angles=np.linspace(0, np.pi, 32, False),
+        )
+    with pytest.raises(ValueError):
+        A = XRayTransform2D(
+            input_shape=(16, 16),
+            det_count=16.3,
+            det_spacing=1.0,
+            angles=np.linspace(0, np.pi, 32, False),
+        )
+    with pytest.raises(ValueError):
+        A = XRayTransform2D(
+            input_shape=(16, 16),
+            det_count=16,
+            det_spacing=1.0,
+            angles=np.linspace(0, np.pi, 32, False),
+            device="invalid",
+        )
+
+
 def test_ATA_call(testobj):
     # Test for the call-based interface
     Ax = testobj.A(testobj.x)
@@ -280,6 +315,13 @@ def test_convert_from_scico_geometry(test_geometry):
     np.testing.assert_allclose(vectors[0, 6:], proj_geom_truth["Vectors"][0, 6:])
 
 
+def test_vol_coord_to_world_coord():
+    vol_geom = scico.linop.xray.astra.astra.create_vol_geom(16, 16)
+    vc = np.array([[0.0, 0.0], [1.0, 1.0]])
+    wc = scico.linop.xray.astra.volume_coords_to_world_coords(vc, vol_geom)
+    assert wc.shape == (2, 2)
+
+
 def test_ensure_writeable():
     assert isinstance(_ensure_writeable(np.ones((2, 1))), np.ndarray)
     assert isinstance(_ensure_writeable(snp.ones((2, 1))), np.ndarray)

scico/test/linop/xray/test_svmbir.py

@@ -60,7 +60,7 @@ def pytest_generate_tests(metafunc):
 
 
 def make_im(Nx, Ny, is_3d=True):
-    x, y = snp.meshgrid(snp.linspace(-1, 1, Nx), snp.linspace(-1, 1, Ny))
+    x, y = snp.meshgrid(snp.linspace(-1, 1, Nx), snp.linspace(-1, 1, Ny), indexing="ij")
 
     im = snp.where((x - 0.25) ** 2 / 3 + y**2 < 0.1, 1.0, 0.0)
     if is_3d: